diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml index 944c9dc1..6014bf02 100644 --- a/openapi/v1/job.yaml +++ b/openapi/v1/job.yaml @@ -324,7 +324,7 @@ paths: description: |- In order to import a file as an attachment to a study, please fill in the following fields: - * `source` - file source with the following possible values: `S3`, `HTTP`, `LOCAL`. + * `source` - The source parameter is ignored and will be removed in version 1.61. The source is automatically extracted from the link. * `dataLink` - a link to a file to import as an attachment. The file will be associated with a study and will be searchable by its name and metadata. * `metadataLink` - an optional URL of a metadata file to be used as the original metadata diff --git a/openapi/v1/odmApi.yaml b/openapi/v1/odmApi.yaml index dd4e9156..33675920 100644 --- a/openapi/v1/odmApi.yaml +++ b/openapi/v1/odmApi.yaml @@ -16067,22 +16067,23 @@ paths: /api/v1/jobs/import/file: post: description: "In order to import a file as an attachment to a study, please\ - \ fill in the following fields:\n\n* `source` - file source with the following\ - \ possible values: `S3`, `HTTP`, `LOCAL`.\n* `dataLink` - a link to a file\ - \ to import as an attachment.\nThe file will be associated with a study and\ - \ will be searchable by its name and metadata.\n* `metadataLink` - an optional\ - \ URL of a metadata file to be used as the original metadata\nfor the created\ - \ objects. The file must contain a single record describing the uploaded attachment.\n\ - * `studyAccession` - an accession of a study the file will be associated with.\n\ - * `dataClass` - file data class with the following possible values: `Bulk\n\ - transcriptomics`, `Single-cell transcriptomics`, `Differential abundance (FC,\n\ - pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single-cell proteomics`,\ - \ `Metabolomics`,\n`Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`,\ - \ `Imaging features`,\n`Gene panel data`, `Biomarker data`, `Physical measures`,\ - \ `Blood counts`, `Other body\nfluid counts`, `Nanopore`, `Flow Cytometry\ - \ (FCS)`, `Document`, `Other`.\n\nWhen job finishes successfully the following\ - \ **result** object can be obtained using `GET /job/{id}/output` request:\n\ - \n```\n{\n \"accession\": \"GSF1234567\"\n}\n```" + \ fill in the following fields:\n\n* `source` - The source parameter is ignored\ + \ and will be removed in version 1.61. The source is automatically extracted\ + \ from the link.\n* `dataLink` - a link to a file to import as an attachment.\n\ + The file will be associated with a study and will be searchable by its name\ + \ and metadata.\n* `metadataLink` - an optional URL of a metadata file to\ + \ be used as the original metadata\nfor the created objects. The file must\ + \ contain a single record describing the uploaded attachment.\n* `studyAccession`\ + \ - an accession of a study the file will be associated with.\n* `dataClass`\ + \ - file data class with the following possible values: `Bulk\ntranscriptomics`,\ + \ `Single-cell transcriptomics`, `Differential abundance (FC,\npval, etc.)`,\ + \ `Pathway analysis`, `Proteomics`, `Single-cell proteomics`, `Metabolomics`,\n\ + `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging\ + \ features`,\n`Gene panel data`, `Biomarker data`, `Physical measures`, `Blood\ + \ counts`, `Other body\nfluid counts`, `Nanopore`, `Flow Cytometry (FCS)`,\ + \ `Document`, `Other`.\n\nWhen job finishes successfully the following **result**\ + \ object can be obtained using `GET /job/{id}/output` request:\n\n```\n{\n\ + \ \"accession\": \"GSF1234567\"\n}\n```" operationId: "startImportAFile" requestBody: content: diff --git a/openapi/v1/schemas/job/ImportAFileRequest.yaml b/openapi/v1/schemas/job/ImportAFileRequest.yaml index 8ae55984..eb4ec551 100644 --- a/openapi/v1/schemas/job/ImportAFileRequest.yaml +++ b/openapi/v1/schemas/job/ImportAFileRequest.yaml @@ -1,5 +1,4 @@ example: - source: HTTP metadataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-object-metadata.tsv dataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-object.pdf studyAccession: GSF334953 @@ -12,6 +11,7 @@ properties: - LOCAL example: HTTP type: string + description: The source parameter is ignored and will be removed in version 1.61. The source is automatically extracted from the link metadataLink: example: https://mybucket.s3.amazonaws.com/my-experiment/my-object-metadata.tsv type: string diff --git a/openapi/v1/schemas/job/ImportExpressionSignalRunRequest.yaml b/openapi/v1/schemas/job/ImportExpressionSignalRunRequest.yaml index 34521e0c..138236c9 100644 --- a/openapi/v1/schemas/job/ImportExpressionSignalRunRequest.yaml +++ b/openapi/v1/schemas/job/ImportExpressionSignalRunRequest.yaml @@ -1,7 +1,6 @@ allOf: - $ref: "#/components/schemas/ImportSignalRunRequest" example: - source: HTTP metadataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-omics-metadata.tsv dataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-omics-data.gz templateId: GSF334953 diff --git a/openapi/v1/schemas/job/ImportMetadataRequest.yaml b/openapi/v1/schemas/job/ImportMetadataRequest.yaml index 1fc87bd5..d600e38a 100644 --- a/openapi/v1/schemas/job/ImportMetadataRequest.yaml +++ b/openapi/v1/schemas/job/ImportMetadataRequest.yaml @@ -1,5 +1,4 @@ example: - source: HTTP metadataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-object-metadata.tsv templateId: GSF334953 properties: @@ -10,6 +9,7 @@ properties: - LOCAL example: HTTP type: string + description: The source parameter is ignored and will be removed in version 1.61. The source is automatically extracted from the link metadataLink: example: https://mybucket.s3.amazonaws.com/my-experiment/my-object-metadata.tsv type: string diff --git a/openapi/v1/schemas/job/ImportSignalRunRequest.yaml b/openapi/v1/schemas/job/ImportSignalRunRequest.yaml index 2b59063a..9c4194a0 100644 --- a/openapi/v1/schemas/job/ImportSignalRunRequest.yaml +++ b/openapi/v1/schemas/job/ImportSignalRunRequest.yaml @@ -1,6 +1,5 @@ description: import signal data request example: - source: HTTP metadataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-omics-metadata.tsv dataLink: https://mybucket.s3.amazonaws.com/my-experiment/my-omics-data.gz templateId: GSF334953 @@ -13,6 +12,7 @@ properties: - LOCAL example: HTTP type: string + description: The source parameter is ignored and will be removed in version 1.61. The source is automatically extracted from the link metadataLink: example: https://mybucket.s3.amazonaws.com/my-experiment/my-omics-metadata.tsv type: string